Molecular Rearrangement Process Research Articles

Observing Dynamic Conformational Changes within the Coiled-Coil Domain of Different Laminin Isoforms Using High-Speed Atomic Force Microscopy.

Laminins are trimeric glycoproteins with important roles in cell-matrix adhesion and tissue organization. The laminin α, ß, and γ-chains have short N-terminal arms, while their C-termini are connected via a triple coiled-coil domain, giving the laminin molecule a well-characterized cross-shaped morphology as a result. The C-terminus of laminin alpha chains contains additional globular laminin G-like (LG) domains with important roles in mediating cell adhesion. Dynamic conformational changes of different laminin domains have been implicated in regulating laminin function, but so far have not been analyzed at the single-molecule level. High-speed atomic force microscopy (HS-AFM) is a unique tool for visualizing such dynamic conformational changes under physiological conditions at sub-second temporal resolution. After optimizing surface immobilization and imaging conditions, we characterized the ultrastructure of laminin-111 and laminin-332 using HS-AFM timelapse imaging. While laminin-111 features a stable S-shaped coiled-coil domain displaying little conformational rearrangement, laminin-332 coiled-coil domains undergo rapid switching between straight and bent conformations around a defined central molecular hinge. Complementing the experimental AFM data with AlphaFold-based coiled-coil structure prediction enabled us to pinpoint the position of the hinge region, as well as to identify potential molecular rearrangement processes permitting hinge flexibility. Coarse-grained molecular dynamics simulations provide further support for a spatially defined kinking mechanism in the laminin-332 coiled-coil domain. Finally, we observed the dynamic rearrangement of the C-terminal LG domains of laminin-111 and laminin-332, switching them between compact and open conformations. Thus, HS-AFM can directly visualize molecular rearrangement processes within different laminin isoforms and provide dynamic structural insight not available from other microscopy techniques.

Photocatalytic Degradation of the Antibiotic Sulfamethazine Using Decatungstate Anions in an Aqueous Solution: Mechanistic Approach

The aim of this study is to propose a successful method for the treatment of water contaminated by pharmaceutical pollutants through homogeneous photocatalysis in the presence of decatungstate ions (W10O324−). Sulfamethazine (SMZ), a sulfonamide antibiotic, was used as a model molecule. The results showed that SMZ could be effectively degraded with this process under simulated solar irradiation. SMZ degradation kinetics were studied with different dioxygen and SMZ concentrations, pH values, and photocatalyst masses. Optimal conditions were determined to be pH 7, [Na4W10O32] = 0.33 g/L, and [SMZ] = 13.9 mg/L under the aerated condition, resulting in 85% SMZ degradation in 240 min, using a 36W-UVA/UVB light source. Hydroxyl radicals were identified as the major contributors to SMZ elimination. Four photoproducts identified with high-performance liquid chromatography coupled with mass spectrometry were formed by the cleavage of the sulfonamide bond and the hydroxylation of both the aromatic ring and pyrimidine moiety. SMZ was completely mineralized after 90 h of irradiation in the presence of decatungstate anions. These results provided a mechanism for the photocatalytic degradation of SMZ in an aqueous solution. To sustain this mechanism, theoretical studies were carried out using density functional theory calculations. This involved Fukui functional analyses, including ring hydroxylation, C-S bond cleavage, and molecular rearrangement processes.

Insights on the Structure in Solution of Paramagnetic LnIII/GaIII 12-Metallacrown-4 Complexes Using 1D 1H NMR and Model Structures.

The solution structure of LnIIINaI(OBz)4[12-MCGaIII(N)Shi-4] complexes was studied through paramagnetic 1H NMR and DFT models. Although isostructural in the solid state, their 1H NMR spectra in DMSO-d6 are extremely different from one another due to the magnetic anisotropy of the lanthanide(III) ions. NMR data were analyzed by the "all-lanthanide" method that were compared to X-ray structures and model structures, allowing to establish the extent of the structural changes that occur from the solid state to the solution phase. Major structural changes involve the phenyl groups of the benzoate ions that, quite surprisingly, in solution present preferential orientations lowering the symmetry of the complex contrary to what observed in the solid state. Overall, DFT methods and 1D NMR data allowed us to clarify aspects related to molecular rearrangement processes in solution that could not be predicted by a simple look at the X-ray structures of these complexes.

Imaging Reconfigurable Molecular Concentration on a Graphene Field-Effect Transistor.

The spatial arrangement of adsorbates deposited onto a clean surface under vacuum typically cannot be reversibly tuned. Here we use scanning tunneling microscopy to demonstrate that molecules deposited onto graphene field-effect transistors (FETs) exhibit reversible, electrically tunable surface concentration. Continuous gate-tunable control over the surface concentration of charged F4TCNQ molecules was achieved on a graphene FET at T = 4.5K. This capability enables the precisely controlled impurity doping of graphene devices and also provides a new method for determining molecular energy level alignment based on the gate-dependence of molecular concentration. Gate-tunable molecular concentration is explained by a dynamical molecular rearrangement process that reduces total electronic energy by maintaining Fermi level pinning in the device substrate. The molecular surface concentration is fully determined by the device back-gate voltage, its geometric capacitance, and the energy difference between the graphene Dirac point and the molecular LUMO level.

Redox-enhanced hemilability of a tris(tert-butoxy)siloxy ligand at cerium.

The stabilizing effect of a tris(tert-butoxy)siloxy ligand on cerium(iv) is revealed by electrochemical and computation methods as well as by targeted redox chemistry. Ceric homoleptic complex Ce[OSi(OtBu)3]4 was obtained by the reaction of [Et4N]2[CeCl6] with NaOSi(OtBu)3 at ambient temperature in acetonitrile, while cerous ion-separated complex [Ce{OSi(OtBu)3}4][K(2.2.2-crypt)] was readily synthesized from [Ce{OSi(OtBu)3}4K] and cryptand. The solid-state structures of monocerium complexes Ce[OSi(OtBu)3]4 and Ce[OSi(OtBu)3]4(THF) show 5- and 6-coordinate CeIV centers (one κ2-bonded siloxy ligand), while complex [Ce{OSi(OtBu)3}4][K(2.2.2-crypt)] exhibits a 4-coordinate CeIII center (all-terminal siloxy coordination). A comparative electrochemical study of Ce[OSi(OtBu)3]4 and [Ce{OSi(OtBu)3}4][K(2.2.2-crypt)] suggests a redox-modulated molecular rearrangement process, featuring oxidation-state dependent formation and release of a CeOtBu coordination. While the overall stabilization of CeIV by the siloxy ligand is evident, significant extra stabilization is gained if the siloxy ligand coordinates in a chelating fashion, which is further supported by DFT calculations. Natural bond orbital (NBO) analysis indicates an enhanced donation of the siloxy ligand electron density into the unfilled CeIV 6s, 4f, and 5d orbitals. CeIV to CeIII reduction readily occurs when homoleptic complex Ce[OSi(OtBu)3]4 is treated with cobaltocene, affording the separated ion pair [Ce{OSi(OtBu)3}4][CoCp2], featuring exclusive terminal siloxy bonding in the solid-state, similar to that detected for [Ce{OSi(OtBu)3}4][K(2.2.2-crypt)].

A kinetic investigation and X-ray analysis of thermal shrinkage of diphenyl carbazide

The kinetics of thermal shrinkage of diphenyl carbazide (DPC) is investigated above and below room temperature by thermo-mechanical analysis (TMA) at various constant rates of heating. The contraction measurements include two temperature regions. The first lies above 0 °C up to ≈53 °C. The second lies below 0 °C and extended down to −165 °C using liquid nitrogen. Two-stage model is applied here to analyze the TMA data. The activation energy of contraction reaction could be obtained from the TMA curves at different heating rates and found to be 30 Kcal/mol for high temperature thermal shrinkage and 2.7 Kcal/mol for low temperature one. The study reveals the presence of two different characteristic shrinkage anomalies above and below zero temperature for amorphous DPC. This contraction behaviour is attributed to the various kinds of molecular motion of this rigid organic structure. X-ray analysis showed that the shrinkage in amorphous DPC samples ceases behind 50 °C where the amorphous state change to monoclinic crystal structure with a = 15.037 Å, b = 8.242 Å, c = 12.760 Å and α = γ = 90° and β = 99.25° with a space group P21/A. Also, X-ray analysis showed that the low temperature shrinkage is not due to a crystal structure change but can be attributed to a molecular rearrangement process of DPC molecules.

Effect of controlled gelatinization in excess water on digestibility of waxy maize starch

Abstract An aqueous dispersion of waxy maize starch (5%, w/w) was controlled gelatinized by heating at various temperatures for 5 min. The treated samples were analysed using in vitro Englyst assay, light microscopy, differential scanning calorimetry, X-ray diffraction, and Fourier-transform infrared spectroscopy. When heated, SDS and RS levels were decreased inversely with RDS. A high SDS content (>40%) was kept prior to the visible morphological and structural changes (before 60 °C). Swelling factor began to increase slightly at 50–60 °C and continued to maximum value at 80 °C. A large decrease in ΔH, crystallinity, and ratio of 1047/1022 cm−1 attributed to partially dissociation of crystalline clusters and double helices occurred at 65–80 °C. These changes showed that controlled gelatinized starch with slow digestion property occurred in the molecular rearrangement process before granule breakdown and SDS mainly consists of amorphous regions and a small portion of less perfect crystallites.

Structure and Dynamics of Methyl-substituted Beryllocene: [Be(C5Me5)2

In this paper we study theoretically the molecular structure of [Be(C5Me5)2], with special interest in similarities and differences found in the computed geometric parameters, depending on the treatment of the electron correlation used. Given the low energy differences found between the different configurations studied (less than 4 kcal mol−1), and the high fluxionality found in experimental studies for this compound, we analyzed the dynamics of the system by means of first principles molecular dynamics calculations. A complex dynamics is found and analyzed in terms of two molecular rearrangement processes: 1,2-sigmatropic intraring rearrangement and a ring inversion mechanism that interchanges the roles (with regard to their coordination to the central Be atom) of the two rings.

Dynamic and morphological investigation of phospholipid monolayer hydrolysis by phospholipase C

The hydrolytic reaction of l-α-dipalmitoylphosphatidylcholine ( l-DPPC) monolayer catalyzed by phospholipase C (PLC) has been investigated using monomolecular membrane technique and Brewster angle microscopy (BAM) at the air/water interface. The curves of surface pressure as a function of time determined a lag-burst process of l-DPPC monolayer hydrolysis by PLC. The BAM images recorded the changes of domains formed in the coexistence region of liquid-condensed (LC) and liquid-expanded (LE) phases during the monolayer hydrolysis. The changes of domain shape and size and the increase of domain number reflect the decrease of reactant and molecular rearrangement process of the main hydrolysis product, dipalmitoylglycerol (DPG). A new phase was observed after the hydrolysis reaction was completed.

Stress relaxation behaviour of dipalmitoyl phosphatidylcholine monolayers spread on the surface of a pendant drop

Dipalmitoyl phosphatidylcholine (DPPC) monolayers were characterised by surface pressure/area isotherms ( π/ A) and surface dilational rheological parameters at temperatures 20–40°C. The methods used were the Langmuir trough and the pendant drop micro-film balance. The latter allows accurate measurements at higher temperatures and transient drop deformation. Stable DPPC monolayers were found only for low surface pressures, π<15 mN m −1. At higher monolayer compression π decreases over a long time, mainly caused by molecular rearrangement processes in the monolayer starting in the coexisting region. At π>25 mN m −1 and 20°C relaxation experiments give evident of rupturing, brittle monolayer structures. At higher temperatures the monolayers became more fluid-like. π/ A-isotherms determined by using both methods principally agree with each other, but show also remarkable differences, which cannot be explained so far satisfactory. Transient drop relaxation experiments were analysed for the short time range (600 s). At 20°C the dilational modulus ( ε r) and the surface dilational viscosity ( ξ r) passes a stationary maximum at 0.54 nm 2 molecule −1 and increase strongly at higher surface coverage, thus indicating crystalline monolayer structure. Increasing temperature from 20 to 30°C causes a rapid decrease of ε r and ξ r and a shift of the stationary maximum to lower surface coverage. No evidence for crystalline structure is found. Further increase of temperature causes ε r and ξ r increase again. This increase is caused by a rising relaxation time, while the elasticity does not change in the same manner. Such intermediate decrease of ε r and ξ r in the range 30–40°C appears to be unusual and can be interpreted as a consequence of strong DPPC interactions and strongly pronounced retardation of monolayer deformation. The study is discussed in connection to the physiology of breathing. For pulmonary surfactants the observed behaviour seems to be understandable. It is however interesting that such complex behaviour is observed for monolayers consisting of DPPC only.

Interfacial dilational behaviour of adsorbed β-lactoglobulin layers at the different fluid interfaces

β-Lactoglobulin adsorption layers at the interfaces solution/air, /tetradecan and /sunflower oil were characterised by dynamic interfacial tension measurements and harmonic drop oscillation experiments in a time scale of some seconds. Axialsymmetric drop shape analysis (ADSA) was used to calculate drop volume, area and interfacial tension. Within a definite range of drop volume amplitude, the oscillation of the surface tension is harmonic and interfacial dilation parameters can be determined. Dependence of the dilational parameters on the amplitude and frequency of drop volume oscillation were determined and methodical demands are given for this special kind of ADSA application. The concentration of interfacial saturation is minimal at the interface with sunflower oil. Interfacial dilational elasticities, and viscosities are maximal at the saturation concentration of all systems investigated. The dilational viscosities are maximal in the frequency range 0.007–0.011 Hz and characterise molecular rearrangement processes in the adsorption layer. Interfacial dilational elasticity and viscosity are the largest at the interface with air. They are the smallest at the interface with sunflower oil. Similarities and differences of the systems investigated are discussed by taking into account the adsorption behaviour and the solvatation of different apolar and polar parts of the protein molecules in the neighbouring phase.

Generation and extinction of a crystal nucleus below the glass transition temperature

The generation/extinction phenomenon of a crystal nucleus was studied for 4-dibenzylamino-2-methylbenzaldehyde-1, 1-diphenylhydrazone by using a differential scanning calorimeter at 120 - 450 K. Glass transition and fusing temperatures were found to be and , respectively, at the heating rate of . Bulk crystallization, observed in the range 390 - 400 K, was used to check whether the crystal nucleation did or did not proceed at low temperatures. The effective nucleus which had a radius larger than the critical value at 290 K was generated through annealing the sample for 1 h in the range 120 - 280 K or for 5 min at 170 - 270 K. The crystal nucleation process was thus found to proceed even at 120 K, lower by 186 K than the . This is interpreted as indicating that the nucleation rate is controlled by the characteristic time of the -molecular rearrangement process which could be much shorter than the annealing period. The crystal nucleus generated during the annealing at 220 K for 1 h was found to be extinguished by rapid heating to temperatures above 300 K. This is qualitatively understood from a classical theory.

β-Molecular Rearrangement Process, But Not an α-Process, as Governing the Homogeneous Crystal-Nucleation Rate in a Supercooled Liquid

Abstract The time dependence of the growth rate of homogeneous-nucleation-based (HNB) crystallization in o-terphenyl was tracked by a temperature-jump method through microscopic observations, and HNB crystallization was found to proceed at a steady rate, specified by the tracking temperature just after the jump. Two sets of numerical computations were carried out according to a classical homogeneous nucleation theory for the temperature-jump experiment on alternative assumptions that the homogeneous nucleation process is governed by the α-molecular rearrangement process or by the β-process in the liquid. From a comparison between the experimental and calculated results, the homogeneous nucleation, and thus the crystal growth as well, were concluded to be governed by the β-rearrangement process rather than the α-process, differently from the common recognition that they are governed by the latter.

Vibronic state symmetry, selection rule and transition probabilities for a molecular rearrangement process. The butadiene-cyclobutene rearrangement

Permutation-inversion group theory is applied to the classification of vibronic states, selection rules, and transition probabilities for a molecular rearrangement process in which the nuclear configuration of the molecule changes substantially. The advantage of the permutation-inversion group in this respect is that it is independent of any particular nuclear configuration.

Viscous liquids and the glass transition. V. Sources of the excess specific heat of the liquid

The possibility that the excess ’’configurational’’ specific heat ΔCp of liquids above the glass transition temperature Tg might contain contributions either from changes in vibrational frequencies with configurational state, from changes in the anharmonicity of vibrations, or from the influence of changes in configurational state on the thermodynamic contributions of molecular rearrangement processes that also give rise to secondary relaxations below Tg is investigated with the use of calorimetric data on six quenched and annealed glasses. It is concluded that at least half of ΔCp arises from these sources, the greater part of this either from anharmonicity or from the molecular rearrangement processes.

Flow Birefringence Measurements in Low‐Viscosity Liquids with the Help of Boundary Layer Shear Waves; and Orientational Relaxation in n‐Alkyl Carboxylic Acids (Normal Fatty Acids)

AbstractA new measuring method for determining flow birefringence constants by generating shear velocity gradients with the help of Rayleigh boundary layer shear waves (21.3 kHz) will be described. This method has an advantage over previous measuring systems with Couette apparatuses in that disturbing heating influences in the birefringent layer can be avoided by pulsed excitation and faulty depolarizations can be eliminated by narrow‐band filtering.With this technique flow birefringence was investigated in n‐heptanoic, n‐octanoic, n‐nonanoic acid, o‐dichlorobenzene and cinnamaldehyde. The temperature dependency of flow birefringence in the carboxylic acids will be discussed on the basis of the theory of Peterlin and Stuart which leads to a simple relation between flow birefringence and orientational relaxation in low molecular liquids. The results will be compared with flow birefringence measurements in n‐paraffins and with investigations of orientational Rayleigh scattering in n‐alkyl bromides. The comparison leads to a confirmation of Peterlin's and Stuart's theoretical starting point. In addition it will be shown that molecular rearrangement processes in n‐alkyl carboxylic acids beginning with propionic acid are carried out predominantly by dimers, whereby the Arrhenius activation enthalpies of these processes are dependent on the molecular chain length in a way comparable to other simple n‐alkyl families.

The kinetics of the thermal decomposition of normal paraffin hydrocarbons II. Comparative measurements on the series from propane to n -decane

The rates of the nitric oxide-inhibited decompositions of hydrocarbons in the series propane to n -decane (which according to the results of Part I represent the chain-free molecular reactions) have been measured over a range of pressures. As inferred from the 'apparent chain length' the molecular rearrangement process increases in importance relatively to the chain reaction with the ascent of the series, and, for a given hydrocarbon, with increasing pressure. For each hydrocarbon, the order of reaction varies between the first and the second. The results are not consistent with a constant order of 1.5 as has been suggested. Nor is the pressure dependence consistent with the uniform transition from second order to first predicted for unimolecular reactions dependent upon a single mode of activation by collision. There appears to be a contribution to the overall reaction from processes which remain of second order up to high pressures. The decomposition rate for a given hydrocarbon pressure tends to a limit as the series is ascended, for reasons which are discussed.